myRT
Top 15 domains that tend to co-occur with UG12 RT in their genomic neighborhood
Note 1: Specificity score -- ranges between 0 and 1, with 1 indicating that a domain is exclusively associated with UG12 RT.Note 2: X*2, if found in the table, either means one gene has two consecutive X domains or two adjacent genes both have X domain.
Note 3: If two instances of a domain X are found in the neighborhood of a particular RT R, it will be counted as 2 occurences of domain X, but 1 co-occurance of X and R).
Note 4: click on 'link' to retrieve all genomes that contain the domain, and 'piechart' to see this domain's distribution among different RTs (including UG12).
| complete genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG12 | 94 (100%) | 1 (94/94) | link | piechart |
| SurA_N_3 (pfam13624) | 9 (10%) | 0.643 (9/14) | link | piechart |
| peptidyl-prolyl cis-trans isomerase SurA (PRK10770) | 9 (10%) | 0.6 (9/15) | link | piechart |
| PRK12904 (preprotein translocase subunit SecA; Reviewed) | 9 (10%) | 0.692 (9/13) | link | piechart |
| UDG (smart00986) | 6 (6%) | 0.857 (6/7) | link | piechart |
| TAS_TAS_TAS_TIGR02293 | 6 (6%) | 0.667 (6/9) | link | piechart |
| PinE (COG1961) | 5 (5%) | 0.016 (5/316) | link | piechart |
| PHA02517 (putative transposase OrfB; Reviewed) | 5 (5%) | 0.002 (5/2144) | link | piechart |
| INT_C_like_1 (cd01184) | 5 (5%) | 0.106 (5/47) | link | piechart |
| emrE (PRK09541) | 5 (5%) | 0.263 (5/19) | link | piechart |
| UvrD (COG0210) | 4 (4%) | 0.075 (4/53) | link | piechart |
| S14_ClpP_1 (cd07016) | 4 (4%) | 0.667 (4/6) | link | piechart |
| PRK00103 (rRNA large subunit methyltransferase; Provisional) | 4 (4%) | 0.667 (4/6) | link | piechart |
| DegQ (pfam08181) | 4 (4%) | 0.444 (4/9) | link | piechart |
| YjgR (COG0433)*2 | 3 (3%) | 0.273 (3/11) | link | piechart |
| draft genomes | |||
|---|---|---|---|
| Domains | Number of occurrences (%) | Specificity score | Co-occurring RTs |
| RVT-UG12 | 728 (100%) | 1 (728/728) | link | piechart |
| YjgR (COG0433) | 28 (4%) | 0.173 (27/156) | link | piechart |
| Phage_int_SAM_2 (pfam12834) | 27 (4%) | 0.19 (27/142) | link | piechart |
| Integrase_1 (pfam12835) | 27 (4%) | 0.031 (27/884) | link | piechart |
| SIR2_2 (pfam13289) | 25 (3%) | 0.138 (24/174) | link | piechart |
| cbl (PRK12679) | 24 (3%) | 0.889 (24/27) | link | piechart |
| YjgR (COG0433)*2 | 23 (3%) | 0.183 (23/126) | link | piechart |
| INT_ICEBs1_C_like (cd01189) | 22 (3%) | 0.043 (22/514) | link | piechart |
| UvrD (COG0210) | 21 (3%) | 0.051 (21/413) | link | piechart |
| RMtype1_S_SonII-TRD2-CR2_like (cd17246) | 19 (3%) | 0.062 (12/193) | link | piechart |
| PinE (COG1961) | 18 (2%) | 0.012 (18/1549) | link | piechart |
| HTH_XRE (smart00530) | 18 (2%) | 0.004 (18/4854) | link | piechart |
| INT_C_like_1 (cd01184) | 17 (2%) | 0.057 (17/298) | link | piechart |
| Phage_int_SAM_3 (pfam14659) | 15 (2%) | 0.069 (15/216) | link | piechart |
| YbjD (COG3593) | 14 (2%) | 0.08 (14/175) | link | piechart |